Fig. 6.
MD simulations demonstrate that aa-tRNA accommodation is sterically blocked by EVN preventing EF-Tu disengagement. aa-tRNA accommodation was measured by the reaction coordinate Relbow (distance between O3′ of U60 and U8 of the A-site and P-site tRNA, respectively), accommodation was considered complete when Relbow of ∼25 Å. (A) Single trace of Relbow during the first 30 million time steps (Left) and a population histogram of 60 simulations (Right) in the absence of antibiotics. (B) Single trace of Relbow during the first 30 million time steps (Left) and a population histogram of 60 simulations (Right) in the presence of EVN. An additional population in the presence of EVN is observed at an Relbow of ∼30 to 38 Å. (C) Structural representation of the additional population observed in the presence of EVN revealing the steric block that EVN imposes on aa-tRNA accommodation (Left) and the interactions that are maintained between domain II of EF-Tu and the aa-tRNA (Right).